Weimin Zhao,
It's not possible to use Trinity output directly with Cuffcompare.
You'll need to map your Trinity transcripts back to your reference genome using
something like Blat or Lastz, convert the mapped transcripts to GTF format, and
then run Cuffcompare.
You can run Lastz in Galaxy, bu
hi, I want to use Cuffcompare to compare my assembled transcripts to a
reference annotation. My assembled transcripts is a Fasta format produced by
trinity, but Cuffcompare requried GTF file , so what should I do? Thank you!
weimin zhao___
T
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